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Relevant bibliographies by topics / Molecular modelling / Dissertations / Theses

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Dissertations / Theses on the topic 'Molecular modelling'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Illa, Tuset Sílvia. "Molecular modelling of quatsome nanovesicles." Doctoral thesis, Universitat Autònoma de Barcelona, 2019. http://hdl.handle.net/10803/667197.

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This thesis is devoted to the theoretical and computational study at atomistic and molecular scales of the properties of novel organic nanoparticles called “Quatsomes” (vesicles made by mixing CTAB cationic surfactant and cholesterol) as well as the interactions of Quatsomes with different types of fluorescent molecules. The methodology employed is computational molecular modelling. It includes modelling of the interactions between molecules at different scales and resolutions (DFT electronic structure calculations, atomistic molecular mechanics force fields and coarse-grain molecular mechanic

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2

Stansfield, Phillip James. "Molecular modelling of potassium channels." Thesis, University of Leicester, 2007. http://hdl.handle.net/2381/29963.

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This study uses the structural coordinates of the determined K+ channels to create comparative models of three diverse members of this family, with the aim of enabling a better understanding of the function of these channels. The K+ channel of primary interest is the hERG K+ channel. The pharmacology of this channel is of considerable interest as serendipitous block of K+ conduction pore may result in cardiac arrest. A set of known antagonists have been docked into novel comparative models of hERG to propose how these drugs interact with the channel. The models have also been subjected to mole

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3

Breed, Jason. "Molecular modelling of ion channels." Thesis, University of Oxford, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308690.

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4

Peng, B. "Molecular modelling of petroleum processes." Thesis, University of Manchester, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.515182.

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5

Park, N. "Modelling shocks using molecular dynamics." Thesis, Cranfield University, 2011. http://dspace.lib.cranfield.ac.uk/handle/1826/5826.

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The study of shocks in solid, crystalline metals has been ongoing since the early works of Rankine and Hugoniot in the latter half of the 19th century. However, the understanding of the behaviour of such materials under these extreme conditions remains an area of active research because of the paucity with which models can predict experimental observations. The modern era has seen a huge increase in the ability to solve many of the problems of this area of study by numerical, rather thatn analytic, means. One of these tools has been the use of computers to provide a numerical solution to the m

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6

Hall, Benjamin A. "Methods for Multiscale Molecular Modelling." Thesis, University of Oxford, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.504367.

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7

Christopher, David. "Molecular dynamics modelling of nanoindentation." Thesis, Loughborough University, 2002. https://dspace.lboro.ac.uk/2134/6924.

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This thesis presents an atomic-scale study of nanoindentation, with carbon materials and both bcc and fcc metals as test specimens. Classical molecular dynamics (MD) simulations using Newtonian mechanics and many-body potentials, are employed to investigate the elastic-plastic deformation behaviour of the work materials during nanometresized indentations. In a preliminary model, the indenter is represented solely by a non-deformable interface with pyramidal and axisymmetric geometries. An atomistic description of a blunted 90° pyramidal indenter is also used to study deformation of the tip, ad

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8

Lumley, James Andrew. "Molecular modelling of biological activity." Thesis, University of Reading, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.393752.

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9

Grant, Guy Hamilton. "Molecular modelling of silicon compounds." Thesis, University of Liverpool, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.329403.

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10

Smith, Derek John. "Molecular modelling of antifreeze proteins." Thesis, University of York, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313768.

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11

Tyrrell, Graham Philip. "Modelling the myosin molecular motor." Thesis, University of York, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.247144.

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12

Theodorou, Doros Nicolas. "Molecular modelling of polymeric glasses." Thesis, Massachusetts Institute of Technology, 1985. http://hdl.handle.net/1721.1/15293.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1985.<br>MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE.<br>Bibliography: leaves 193-199.<br>by Doros Nicolas Theodorou.<br>Ph.D.

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13

Searle, Stephen M. J. "Molecular modelling of immunoglobulin folds." Thesis, University of Bath, 1997. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246005.

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14

Richardson, Kevin John. "Submillimetre molecular line observations and modelling of molecular clouds." Thesis, Queen Mary, University of London, 1985. http://qmro.qmul.ac.uk/xmlui/handle/123456789/1705.

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Submillimetre molecular line observations of molecular clouds in our galaxy are presented, and the data analysed using various alternative cloud models. A critical review is given of the methods commonly used to interpret molecular line data, including both theoretical considerations and issues relating to calibration and comparability of results obtained with different telescopes. A detailed comparison is made between results predicted from large velocity gradient (LVG) models, including the generalisation to non-monotonic velocity flows, and those given by "microturbulent" clouds. An LVG mod

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15

Pérez, Mirón Javier. "Molecular Modelling of Switchable[2]Rotaxanes." Doctoral thesis, Universitat Autònoma de Barcelona, 2008. http://hdl.handle.net/10803/3278.

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En aquesta tesi s'ha desenvolupat i utilitzat una potent estrategia computacional per a l'estudi, tant estructural, dinàmic i energètic, de nous [2]rotaxanes que van ser sintetizats i caracteritzats experimentalment pel grup de recerca col·laborador del Prof. Donald Fitzmaurice de la University College Dublin, a Irlanda. Com a etapa preliminar, es van estudiar uns pseudorotaxans formats per les mateixes estacions que presentaven els nous [2]rotaxans. Es va modelitzar el comportament dels pseudorotaxans en diferents dissolvents (CH3CN i CH3OH) i amb la presència de dos tipus de contraions (PF

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16

Fange, David. "Modelling Approaches to Molecular Systems Biology." Doctoral thesis, Uppsala universitet, Molekylärbiologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-132864.

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Implementation and analysis of mathematical models can serve as a powerful tool in understanding how intracellular processes in bacteria affect the bacterial phenotype. In this thesis I have implemented and analysed models of a number of different parts of the bacterium E. coli in order to understand these types of connections. I have also developed new tools for analysis of stochastic reaction-diffusion models. Resistance mutations in the E. coli ribosomes make the bacteria less susceptible to treatment with the antibiotic drug erythromycin compared to bacteria carrying wildtype ribosomes. Th

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17

Smith, Michael J. "Molecular modelling of MHC/peptide complexes." Thesis, University of Oxford, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297304.

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18

Docherty, Robert. "Modelling the morphology of molecular crystals." Thesis, University of Strathclyde, 1989. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=21215.

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Computer programs have been written which allow morphological calculations based on a knowledge of internal crystal structure to he carried out. Details of the programs are presented along with the guidelines developed for their use. The programs were used to compare and contrast the current methods employed for relating crystal shape to structure and to confront specific problems in that field. Calculations on a range of compounds show that the morphologies derived from the simple Donnay-Harker (DHI) model give almost as good a fit to the observed form as the more sophisticated attachment ene

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19

Hussain, Abrar. "Molecular modelling of protein-ligand interactions." Thesis, University of Nottingham, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.587840.

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In this thesis we discuss the role played by computational methods in drug discovery and present studies chiefly using molecular simulation methodologies to characterise the binding of compounds that may serve as leads for antitumour agents against two separate proteins. We report flexible docking and QSAR studies on aplyronine A, and its analogues, a potent inhibitor of the actin protein system. Our findings delineate the mechanism by which the compounds bind to an actin monomer and highlight key features of the compounds that are fundamental for actin- depolymerisation, which instigates the

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20

Todde, Guido. "Exploring Protein Functions by Molecular Modelling." Doctoral thesis, Stockholms universitet, Institutionen för material- och miljökemi (MMK), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-114401.

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Proteins are one of the most important families of biological macromolecules. Proteins can assume many different structures. This makes them perfect to serve a wide range of functions in all organisms. In the last decades, molecular modeling has become an important and powerful tool in the investigation of biological systems. Adopting different computational methods many protein functions and structure related problems can be explored. This thesis focuses on three different protein issues. The structural changes induced by high temperature on a large enzyme were investigated simulating the den

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21

Betts, Tyrone. "Molecular modelling of calcium modulated proteins." Thesis, University of Newcastle Upon Tyne, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.308880.

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22

Fey, Natalie. "Molecular modelling of ferrocenes and arylphosphines." Thesis, Keele University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368982.

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23

Gong, Luwen. "Molecular characterisation and modelling of hydroprocesses." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/molecular-characterisation-and-modelling-of-hydroprocesses(a2514b5b-93e0-41d2-abbb-6c515774e188).html.

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Petroleum is a valuable natural resource, and it is therefore of great significance to exploit the maximum economic potentials of the hydrocarbon molecules. Under current circumstances, marginal profit of the refining industry is highly affected by heavier and sourer crude oils, stricter environmental regulations, more stringent product specifications and higher market demands of lighter products, all of which emphasize the importance of secondary processes such as hydrotreating and hydrocracking. The lumping methods for process modelling are no longer applicable as they fail to predict proper

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24

Teo, Chuan-Tze. "Conformation and reactivity in molecular modelling." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615977.

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25

Martin, Andrew R. "Molecular modelling of antibody combining sites." Thesis, University of Oxford, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257962.

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Antibodies are capable of high specificity interactions with a virtually infinite range of substrates (antigens). This property has lead to a number of scientific and medical applications. The extreme variability is essentially confined to 6 hypervariable loops or 'CDRs' which constitute the antigen combining site. To make intelligent modifications to antibody affinity and specificity, by methods such as site directed mutagenesis, requires an understanding of the relationship between primary sequence and three dimensional structure of the combining site. A new 'combined algorithm' which makes

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26

Pedersen, Jan T. "Molecular modelling of antibody combining sites." Thesis, University of Bath, 1993. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.332966.

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27

Whitelegg, Nicholas R. J. "Molecular modelling of antibody combining sites." Thesis, University of Bath, 1998. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.300880.

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28

Soprani, Lorenzo <1994&gt. "Molecular modelling of organic functional materials." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2022. http://amsdottorato.unibo.it/10361/1/PhD_Thesis_Soprani.pdf.

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The investigation of the mechanisms lying behind the (photo-)chemical processes is fundamental to address and improve the design of new organic functional materials. In many cases, dynamics simulations represent the only tool to capture the system properties emerging from complex interactions between many molecules. Despite the outstanding progresses in calculation power, the only way to carry out such computational studies is to introduce several approximations with respect to a fully quantum mechanical (QM) description. This thesis presents an approach that combines QM calculations with a

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29

Kalweit, Marco. "Molecular modelling of meso- and nanoscale dynamics." Thesis, Cranfield University, 2008. http://hdl.handle.net/1826/2637.

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Molecular modelling of meso- and nanoscale dynamics is concerned with length and time scales that are in the transition zone from molecular to continuum models. Molecular simulation methods, in particular molecular dynamics (MD), only allow the simulation of relatively small nanoscale systems. Continuum methods, such as computational fluid dynamics (CFD), are applicable at macroscopic scales but cease to be valid for nanoscales. This thesis is focused on hybrid MD-CFD methods with geometrical decomposition that seek to bridge the gap between molecular and continuum modelling. The hybrid soluti

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30

Doughty, Stephen William. "Molecular modelling of voltage-gated calcium channels." Thesis, University of Oxford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362014.

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31

Leeke, Caleb. "Environmental fate prediction using molecular modelling techniques." Thesis, Northumbria University, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.367406.

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32

Jiranusornkul, Supat. "Molecular modelling studies of DNA damage recognition." Thesis, University of Nottingham, 2008. http://eprints.nottingham.ac.uk/11303/.

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How DNA repair proteins search and recognise the rare sites of damage from the massive numbers of normal DNA remains poorly understood. FapydG (2,6-diamino-4-hydroxy-5-formamidopyrimidine) is one of the most prevalent guanine derived lesions involving opening of the imidazole ring. It is typically repaired by formamidopyrimidine-DNA glycosylase (Fpg) as an initial step in base excision repair; if not repaired, the lesion generates a G: C -+ T: A transversion. Unfortunately, studies on the recognition of FapydG have been hindered by difficulties to synthesise and incorporate the FapydG residue

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33

Beevers, Andrew James. "Molecular modelling of self assembled peptide nanostructures." Thesis, University of Leeds, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.275634.

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34

Hadjigeorgiou, Christina. "Molecular modelling studies on bidentate iron chelators." Thesis, King's College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298845.

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35

Qiu, Song. "Molecular communication systems : design, modelling and experimentation." Thesis, University of Warwick, 2017. http://wrap.warwick.ac.uk/95162/.

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Molecular Communications (MC) is an increasingly attractive technique to enable the communication and networking of devices in environments where traditional communication techniques may not be suitable. MC has been used to convey information in both human society and in animal populations and been studied on both the microscale and the macroscale. On the basis of these studies, this thesis focuses on characterising MC channel models under different environments and examining the impact these models have on the communication performance. The thesis begins by reviewing the latest developments i

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36

Uzoh, O. G. "Modelling molecular flexibility for crystal structure prediction." Thesis, University College London (University of London), 2015. http://discovery.ucl.ac.uk/1460832/.

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In the crystal packing of molecules wherein a single bond links aromatic groups, a change in the torsion angle can optimise close packing of the molecule. The improved intermolecular interactions, Uinter, outweigh the conformational energy penalty, ΔEintra, to give a more stable lattice energy, Elatt = Uinter + ΔEintra. This thesis uses this lattice energy model hierarchically in a new Crystal Structure Prediction (CSP) algorithm, CrystalPredictor version 1.6, which varies the low-barrier torsion angles at the start of generating hypothetical crystal structures. The crystal structure of 1-benz

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37

Mitchell, Felicity. "Modelling protein flexibility using molecular simulation methods." Thesis, University of Manchester, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.525167.

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38

Sun, Jianjun. "Molecular modelling and integration analysis of hydroprocessors." Thesis, University of Manchester, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.706487.

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39

Jokiaho, Olli-Pekka. "Spectral modelling of molecular nitrogen in Aurora." Thesis, University of Southampton, 2009. https://eprints.soton.ac.uk/161195/.

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A custom made five panel filter mosaic window was designed, installed and operated with the HiTIES (High Throughput Imaging Echelle Spectrograph) at the Nordlysstasjonen in Svalbard, Norway (78.2025N and 15.829E). The filter provides images of the resonant scattered spectra of N+ 2 1N (0,1), (1,2), (2,3) bands and a neutral N2 2P (0,3) band. Ab initio models were created for describing the populations of vibrational and rotational energy levels in both excited and ionised N2 molecules in the ionosphere. In the rotational profiles the species are treated to be in thermal equilibrium, whereas th

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40

Marques, Igor Oliveira. "Molecular modelling of transmembranar transporters for chloride." Master's thesis, Universidade de Aveiro, 2011. http://hdl.handle.net/10773/7403.

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Mestrado em Biomedicina Farmacêutica<br>Ion transport across cell membranes is crucial for the maintenance of cellular and organic homeostasis. When the ions transport is impaired, several disorders may arise, such as channelopathies. Over the last decade, potential synthetic substitutes for the impaired ion channels have been developed, with the ability to mimetic their functions. In this context, tripodal synthetic molecules incorporating thiourea binding groups were experimentally investigated as anion receptors and transmembranar transporters. The obtained results demonstrated the ab

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41

Liu, Luyi. "Molecular characterisation and modelling for refining processes." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/molecular-characterisation-and-modelling-for-refining-processes(2844bcd8-070c-4f91-ba83-1deb7f1600a7).html.

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The highly competitive market in the oil refining industry forces refiners look for more detailed information of both feedstocks and products to achieve the optimal economic performance. Due to stricter environmental legislations, the molecular level characterisation has been investigated by various researchers and shows promising advantages in modern refinery design and operation. Although various molecular characterisation methods have been developed, there is an unavoidable trade-off between keeping astronomical molecule details and practicality in industrial applications. In the meantime,

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42

Cosoli, Paolo. "Multi-scale molecular modelling for environmental systems." Doctoral thesis, Università degli studi di Padova, 2009. http://hdl.handle.net/11577/3426855.

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This thesis aims at exploring the potentialities of multiscale molecular simulation techniques for studying phenomena and processes of environmental interest. After a first description of the state of the art, relative to the molecular simulation techniques applications in the environmental engineering field, the thesis describes the most commonly employed molecular simulation techniques. The applications studied in this thesis are described in order to try to represent the following representative areas of interest: • Recycling and requalification of scrap materials • Pollution removal •

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43

Gamblin, Richard James. "Molecular recognition mechanisms in DNA binding protein families, using molecular modelling techniques." Thesis, University of Leeds, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.436398.

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44

Menche, Gerd. "Molecular modelling Untersuchungen zur Enantiomerentrennung in der HPLC." [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=97430476X.

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45

Fransson, Linda. "Molecular modelling - understanding and prediction of enzyme selectivity." Licentiate thesis, KTH, School of Biotechnology (BIO), 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-10532.

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<p>Molecular modelling strategies for evaluation of enzyme selectivity wereinvestigated with a focus on principles of how molecular interactionscould be evaluated to provide information about selectivity. Althoughmolecular modelling provides tools for evaluation of geometrical andenergy features of molecular systems, no general strategies for evaluationof enzyme selectivity exist. Geometrical analyses can be based uponinspection and reasoning about molecular interactions, which provide aneasily accessible way to gain information, but suffer from the risk of biasput in by the modeller. They can

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46

Hall, Katherine Frances. "Hybrid computational methods for modelling molecular excited states." Thesis, Imperial College London, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.501445.

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47

Swift, Simone. "Molecular modelling of the complex polysaccharide heparan sulphate." Thesis, University of Huddersfield, 2011. http://eprints.hud.ac.uk/id/eprint/10739/.

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Heparan Sulphate plays an important role in many life processes and so an understanding of its role as a universal co-receptor is of great importance. Traditionally oligosaccharides derived from the related molecule heparin have been at the forefront of molecular drug design, due to its similarity in structure and function. To obtain a more complex and detailed picture of the role of HS in structural biology further complex work must be undertaken on HS. Here in this study a number of HS derived octasaccharides have been purified. Alongside this is work carried on HS derived decasaccharides, o

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48

Adcock, Charlotte. "Molecular modelling and electrostatic properties of ion channels." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297941.

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49

Borg, Matthew Karl. "Hybrid molecular-continuum modelling of nano-scale flows." Thesis, University of Strathclyde, 2010. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=14367.

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50

Li, Yazhuo. "Crystallographic and molecular modelling studies of NQO2-complexes." Thesis, University of Nottingham, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.537673.

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